AMIE
by WineDadYoongi
Summary: After years of being alone Sheldon is finally reunited with the love of his live. She however isn't the same as she used to be. -Discontinued.
1. Chapter 1

**A/N: Disclaimer- The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady,**

 **English is not my first language and I have Dyslexia so I would like to apologize for any spelling, grammar or word errors. My bestie and beta reader zeldaslullabiess also isn't English, but thank you for trying anyways!**

 **This is my first/test fanfic if this gets a possitive response I will write more chapters.**

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 **Chapter 1**  
She was listening to the sounds surrounding her, she had been doing so for a couple of minutes now. The soft ticking of the clock made her calm. She heard one part of a phone call, but she couldn't figure out what they were saying. Someone was walking in the room, she could hear the person breathing and coming closer to her. She tried to focus on the clock again, she didn't want to focus on this unknown person. When she couldn't focus on the clock, she tried to remember where she was or who she was, anything, but nothing came to mind, everything before a few seconds ago was a black hole. She had no memories. She didn't want to open her eyes but she knew she had to.

Reluctantly, she opened her eyes only to see a man staring at her. His big blue eyes seemed shiny, like he had been crying. "Amy, you're awake." He stated. Amy. That was her name. It seemed familiar, but she couldn't remember where she had heard it before. "I wasn't sure this would work, I've been trying for a long time." The man continued. She had no idea what he was talking about, but she assumed that it had something to with her and her lack of memory. "Who are you?" She asked.

The man in front of her looked startled. He quickly got himself together before sitting down on the corner of the table she was laying on. "Sorry, your voice startled me." He explained. She nodded for a moment, not really sure why her voice would startle him, but that was the least important thing on her mind right now. "My name is Dr. Sheldon Lee Cooper and I am your husband." He acknowledged.

A slight frown appeared on her face. Her husband? She had no idea who this man was. He could easily be lying to her. She doubted that was true, he genuinely seemed happy to be talking to her.

He seemed to notice her frown. "I know this is a very strange situation, so let me explain what happened." He spoke. Amy nodded. "You were in an accident a couple of years ago, something.." He paused, "bad happened and now you're here, finally awake again." Sheldon explained with a smile on his face. "Your name is Amy Farrah Fowler, you used to be a neurobiologist, you love Chaucer, other medieval poetry, old French movies and Little House on the Prairie." The man continued.

"What bad thing happened to me?" She asked quickly, interrupting him. She wanted to know why she had no memory, why she was lying in a lab, why he said that she was finally awake again, how many time had passed. She figured that it all had to do with what had happened to her and the only person who was able to answer her questions was this guy, named Sheldon.

She heard him let out a soft sigh. "I don't think I should tell you now, you just woke up." He spoke softly. She could hear the insecurity in his voice, however she wanted answers and she would get them one way or another.

"Fine, then I'll leave and find someone else to tell me." She said as she pushed herself up from the table. She expected it to take a lot more effort since she had apparently been asleep for a long time, however her muscles seemed to have no troubles listening to her mind. She quickly scanned the room to see if there was an exit. She had no intention of staying here if he wasn't going to answer her question.

The man immediately shot up as he heard her words. "Amy, please listen to me, you're not yourself yet, you're not used to this yet." He quickly spoke. He raised his hand to lay it on her shoulder but stopped himself before he actually did. She shook her head. "No, you won't tell me what I want to know, so I will find someone who does want to tell me." She stammered as she pushed herself of the bed. Once she was standing and the blanket had fallen off her body she noticed that she was completely naked. She grabbed the blanket from the ground and immediately wrapped it around her body. "Why am I naked?" She quaked with a distressed look on her face.

His eyes quickly scanned her body. He flushed before looking away. "It was easier if you weren't wearing anything." He answered. Somehow she knew she was not going to get a better explanation, at least not now.

She looked down, afraid of what was going to happen, afraid of what had already happened. She held the blanket even tighter. She hadn't been afraid when she woke up, but now she truly was. He didn't seem like a guy who would or could harm her, yet she couldn't forget how he had looked at her just a moment ago.

Before her thoughts went to dark places he handed her some basic clothes, underwear, a bra, shorts and a red t-shirt with a bright yellow symbol on it. "You always loved this T-Shirt and so did I." He said quickly with a shy smile on his face. "I'm sorry for the clothing, I know you will feel exposed in it but it was the only thing I could find on such a short notice." He added. She simply nodded and took the clothes from him. Once she had put on her clothes she noticed that everything seemed to fit her perfectly, except for the red T-shirt, which was too big for her. "It was mine." He said as he noticed her looking at the shirt. "Thank you." She said softly. Her arms were still wrapped around her body, after having just been completely exposed she felt uncomfortable.

"I'll be leaving now." She said. She turned around and made her way to the door, only to be blocked by Sheldon. "Amy, please you cannot leave, you're not ready." He begged. The worried look on his face made and the tone of his voice made her feel odd. Somehow she knew that he would do her any harm. "I promise I will answer all of your questions in time." He continued. She let out a soft sigh. "Okay." She mumbled softly. A smile appeared on his face once again. "Let me bring you back to the table, I must check a few vital signs." He said as he carefully laid his hands on her shoulder and slowly pushed her backwards to the table. She complied. Once at the table Sheldon asked her to lay down again and close her eyes. She was nervous but somehow, she knew that she was safe.

In this short period of time. This strange guy, named Sheldon had already made her feel comfortable again. She knew there was a lot he had to tell her, but in this moment it didn't matter anymore. She knew he would do so in time. For now, she just had to trust and listen to him. She didn't know how, but she knew that everything would be alright if she did.

She closed her eyes and everything was once again completely black. Soon also the sounds surrounding her faded once again and she was gone.

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 **I don't know if this story will be well received, so I only wrote one chapter. I will continue this fanfic if people like it or are curious about the plot.**

 **So please leave a comment.** **The continuation of this story depends on it.**


	2. Chapter 2

**A/N: Disclaimer - The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady.**

 **I really hope that you'll like this chapter. I don't really have experience with writing, so this is something new for me and I'm always nervous before and after uploading because I have no idea if it's good or if people like it not.**

* * *

 **Chapter 2**

The next time Amy opened her eyes, she was in a white room. Nothing was there, except for a blue door with the number 314 on it. She slowly opened the door to see what was inside. A cold gush of wind came from the room, causing her to wrap her arms around herself to preserve body heat. Just like the room before the room was completely empty. However there was something different this time. A man was standing with his back towards her. "Hello?" Amy asked as she took a step closer to him. She heard a soft click of the door closing. She turned around, but the door was nowhere to been seen.

"Amy" The man said. Amy quickly turned around again, this time the man was facing her. It was the same man she had seen before, the day in the lab. Sheldon. "Please don't do this." Sheldon said as he walked towards her. Confused, she looked around, wondering if maybe he was talking to someone else. There was no one in the room besides them. "Do what?" Amy asked curiously.

Sheldon's brows furrowed for a short moment before turning away from her again. "I don't want you to leave, not even for a few days, especially not now." He let out a soft sigh as he sat down on the couch.

A frown appeared on her face as she saw him sitting down. She was sure that the couch hadn't been there before. Her mind was rapidly searching for an explanation of the disappearance of the door and the sudden appearance of the couch. "Why shouldn't I go?" She asked as something forced her to walk to the couch and sit down next to him.

"You're carrying precious cargo, I can't let you out of my sight!" He said as he rested a hand on her stomach. "Precious cargo?" She asked before looking down. She gasped audibly as she saw her stomach. She was pregnant. She knew this couldn't be happening, at least not right now. Once again her mind searched for a logical explanation. The only one she could find was that this was a dream or a memory.

The moment she realized that it was most likely a combination of both the dream started to collapse. Sheldon and the couch both immediately disappeared and she suddenly fell on the ground. Slowly the walls and the ceilings started to collapse, only darkness could be seen behind the white walls. Soon the ground and ceiling had both disappeared and the ground started to give away. She fell into the darkness.

* * *

Her eyes suddenly popped open. She was back at the lab she had been in before. She quickly pushed herself up and let out a long, relieved sigh. "It seems like you were dreaming, interesting." She heard Sheldon mumble. She turned her head to the side, Sheldon was sitting in front of a computer, staring at something that seems like her brain activity. It seemed oddly familiar.

"I was." Amy stated. She quickly checked under the blanket to make sure she was dressed. She was still wearing the clothes from before. A shiver ran down her spine as she touched the cold floor with her feet. "What were you dreaming about?" Sheldon asked, he was still studying the brain activity. "Not much," Amy said as she looked back at him. "I was having a conversation, but I didn't understand most of it, it was a very one sided conversation." She added.

She took the blanket from the table and wrapped it around her. She walked over to Sheldon and looked at the computer screen. She knew it was brain activity but she had no idea what it meant. "May I ask you a question?" She inquired. Sheldon nodded before turning to her.

"What happened to me?" She asked. Sheldon let out a sigh. "I told you, you're not ready for that yet." He replied. "When will I be?" Amy asked quickly. "I honestly don't know." He acknowledged. Amy nodded before walking to another chair in the lab. She let out a deep sigh and slumped down. "How long have I been asleep?" She asked. Once again, she didn't expect an answer.

For a moment the room filled with silence before Sheldon suddenly spoke. "4 years, 7 months, 11 days." He stated. Amy's head suddenly shot up to look at Sheldon again. She had figured that she had been asleep for some time, but not such a long time. A tear ran down her cheek. She quickly wiped it away. She had no reason to cry, she was alive and physically well, she couldn't even remember her previous life, so why should it bother her? "Amy, as I've said before, I know this is a strange situation but trust me, I will explain everything when you're ready." Sheldon begged as he walked over to her. He sat down next to her on the couch, it was similar to what she had done in her dream.

She looked up at the man sitting next to her right now. She had many more questions but only one came to mind in that moment. "Why is it so cold in here?" She asked as she pulled the blanket closer around her body. Sheldon frowned for a moment. "We still need to fix some things." He replied quickly.

Before she could ask another question the door suddenly went open. A tall, not too muscular man walked in to the room and closed the door behind him. "I thought you were going to pick me up? I had to take a cab from the airport." He exclaimed before throwing down his bag. "That child of mine got into trouble again. I find it hard to believe he's my offspring, he's completely useless." The man complained. "Surely, you've had your fun…" The man stopped mid-sentence as he finally noticed her.

Once again silence filled the room before the man finally talked. "We did it?" He asked, barely louder than a whisper. "Yes, I succeeded yesterday." He stated. The man quickly walked towards her and raised his hand to touch her face, she however quickly pulled back and turned to away from him. "Please don't touch my wife, she doesn't like that." Sheldon stated as he grabbed the man's arm away from her face. The man snickered. "Your wife? Does she even know you?" He asked with mocking undertone.

Sheldon flashed him an angry look before walking to another door. "I'd like to talk to you in private." Sheldon demanded. The man let out a deep sigh before following Sheldon to the other room, leaving Amy alone on the couch. Wondering about what had just happened.

* * *

After a few minutes of waiting they still hadn't returned. Amy had gotten off the couch and had started wandering around, looking at the various computers. Most of them were off, except for the one Sheldon had been working on earlier.

She walked over to the computer and looked at the screen. She knew it was brain activity, however this time she also noticed it was playing on a loop, like it had been recorded. A closed file was laying on the table with the letter A.M.I.E on it. She knew she shouldn't be looking at it, Sheldon would explain everything when she was ready but curiosity overtook her and she grabbed the file. She opened the file. Her eyes fell on a picture of a heavily injured woman, she looked familiar but Amy couldn't place where she had seen her before.

Before she could continue looking through the file the door opened and both, the man and Sheldon came out. Out of shock she had dropped the file. "You're wasting our time with such antics. We will submit her to my tests with or without your consent." The man stated. He looked up at her as he heard something fall. "She's curious, she wants to know." He stated.

Amy quickly gathered the paper and put them back in the file. "I'm sorry." She stammered. She put the file back on the table before quickly taking a step back and hanging her head down in embarrassment.

The man walked closer to her. "It's pointless not to tell her, it's a basic human feeling to be inquisitive about trifling matters. However, in this case it is her right." He stated. "Let me introduce myself, my name is Reed Clayton, Doctor Cooper worked with me to fix you." He said. Amy looked up at the man. "Fix me?" She asked a little insecure. "Yes, you see, you d-" "Doctor Clayton!" Sheldon interrupted.

Sheldon hurried to Amy's side and put a hand on her shoulder. She looked over at him with an uncomfortable look on her face. Before she could ask anything everything turned black and she started falling, only to be stopped by both Reed and Sheldon's hands. "She needs to know, in order for me to continue my research." Was the last thing she heard before the darkness had surrounded her and all sounds had once again disappeared.


	3. Chapter 3

**A/N: Disclaimer - The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady.**

 **I hope that everyone will still enjoy this story after this chapter.  
**

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 **Chapter 3**

Amy was standing in a lab, with her lab coat on. She couldn't remember how she had gotten here, but that didn't seem to matter at the moment. "Doctor Fowler, have you taken a look at the files I send?" A man asked. Amy turned around so she could face the man who had asked her a question. Reed Clayton was standing in the room with her, this time he was also wearing a lab coat. "I haven't had the chance, yet." Amy replied.

"A Pity." She heard him mumble. She turned back to face the table in the room. An unknown man was laying on it. "We haven't got all day, hurry up and look at the files." Reed ordered. Amy once again turned around to face the man. "I refuse to be ordered around, we agreed that I would help you with your research on my terms." She snapped back.

After a short moment of staring at each other Reed continued his work and Amy returned to her computer. As she opened the map on the computer she noticed two other projects. Project S.O.P.H.I.E and S.O.P.H.I.A. "Doctor Clayton, care to explain why your old projects have been added?" Amy inquired. "To me the data is worthless, but you might be able to make something of it and use it in order to make our new Project better." He replied.

When Amy had examined both files the day was almost over and Reed started preparing to go home, Amy finally looked up from the screen again. "I've gotten an offer to check out a new study, based on my old work." Amy stated, causing Reed to stop what he was doing and look up at her. "It means that I will leave for a couple of days. I will let you know the exact dates as soon as possible." She continued. "What a waste.." Reed mumbled. "Enjoy your trip Doctor Fowler." He said before walking out the door leaving Amy on her own in the lab.

Amy let out a deep sigh and rested her hand on her belly. She knew Sheldon and Reed both didn't want her to go, both for different reasons of course but it was a great opportunity. Her curiosity had taken over and she accepted it before she actually had thought about the consequences.

* * *

When Amy awoke again she was sitting in a chair and in a different room. It was highly uncomfortable but this did seem like the most comfortable place in the room. She let out a soft groan and she pushed herself up and looked around the room. The room was dimply lit, there were two chairs, a table and a camera.

Before she could continue her examination of the room the door went open and Doctor Clayton came into the room. "Hello Amy, I see you've woken up once again." He stated as he closed the door behind him. "I apologize for the room, but we have limited resources." He said with a forced smile on his face. "Why don't you sit down, so I can ask you some questions." The man said as he made his way over to the other chair and sat down.

Once they were both sitting Reed talked again. "Well.. Shall we begin?" He requested. Amy folded her hands in her lap and straightened her back a little. "I will answer your questions if you answer mine." She answered. A smirk appeared on his face. "Doctor Cooper did mention that this could happen, but very well, I will answer your questions."

Amy let out a soft relieved sigh, she was happy that he had agreed and had been scared that he would have laughed or said that she couldn't ask for anything. After all, she could be seen as a prisoner. "I heard from Doctor Cooper that you've had dreams, what are they about?" Reed asked.

For a moment Amy looked up at Doctor Claytons face. She looked down to her hands as she started talking. "I think they're memories." She stated before looking back up to see his reaction. "My turn," She quickly added. "what happened to me?" She asked curiously. "You died." Reed stated in a monotone voice.

Amy gasped softly. "What? But how?" She asked. "It's not your turn, it's mine." He said. "What were your dreams about?" He inquired. Amy didn't reply to him. She was still in shock to learn about the fact that she had died. It would explain why she couldn't remember, but it didn't how she was sitting here.

"Amy." Reed said a little louder. Amy quickly looked up again. "Euhm.. I dreamed about Doctor Cooper, he didn't want me to leave and once about you, we were working on something, that's all I remember." She answered quickly. "How did I die?" She asked a little insecure. "Monkeys killed you." He said as he scribbled something in his notepad. "Do you know what you were working on or where you were going?" He asked. Amy shook her head. Reed mumbled something incoherent before continuing writing. "Can you tell me what exactly happened?" Amy asked softly.

Reed looked up from his notepad, which he laid down on the table. "The project we were working on failed, you said you had to leave for a couple of days, the escaped project gave the monkeys you were working with the wrong drug and let them escape, they attacked you and you died." He stated quickly. "Now, tell me, do you feel different in your dreams or your memories or does it feel the same." He asked. "I don't think so." She mumbled. "What am I?" She asked. "You're my new project A.M.I.E. It stands for Advanced Mainframe Identity Engine." He explained.

Before Doctor Clayton could ask another question the door went open and an angry looking Sheldon emerged into the room. "I told you not to do this." Sheldon bellowed. Sheldon quickly hurried his way over to Amy. The angry look on his face quickly changed into concern when he saw her shocked expression. "Are you okay?" He asked Amy. Amy shook her head as tears gathered in the corner of her eyes. "I'm taking her home, we're done with your research." Sheldon hissed as he pulled Amy up by her arm.

Amy quickly wiped her eyes with her free hand and looked at both the man. "We haven't finished testing her yet, would you like a recurrence of the previous project, put Amy in danger or your daughter?" Reed asked as he watched Sheldon pull Amy to the door. Sheldon stopped for a moment and considered his words. "I know my wife, she is nothing like your previous project."

The door closed loudly and Reed was left alone in the dim lit room. He let out a deep sigh and shook his head. He knew they would be back.

* * *

About an hour later Amy and Sheldon arrived at an apartment complex in a very bad looking neighborhood. "I am sorry for the state of the neighborhood and the current state of the apartment, I haven't worked in a while and we have to be careful with money." He explained as he gently pushed her inside. Sheldon walked up to the first floor with Amy close behind him.

He had been right to apologize, she thought once she was inside the apartment. It was clean but there were papers everywhere with equations scribbled on them, some children's toys and boxes everywhere. "I haven't had the time yet to unpack or to clean up." He mumbled apologetically. Amy nodded for a moment before making her way over to the couch.

She had no idea what to say or do. She wasn't sure if this was a better or worse situation. She sat down in the corner of the brown couch. "Oh dear.. that's my spot.." Sheldon said but as he saw the expression on his face he let out a soft sigh. "You can sit there for now." He added uncomfortably. "Thank you." Amy said silently.

Sheldon quickly started grabbing the children's toys and put it in a random box. After a couple of minutes he started picking up the papers and put them down on the desk. Amy had in the meantime pulled up her legs and wrapped her arms around them. She was lost in thought about the new information she had gotten today.

"Amy." Sheldon said, causing Amy to look up from the spot she had been staring at. "I have to go pick someone up, please make yourself comfortable, you can take a shower, take a look around the apartment, put on some clean clothes, etcetera." Sheldon said as he grabbed his keys. "I will explain everything in better detail tonight, if you want of course." Amy nodded once again. "Thank you." She mumbled softly again.

Sheldon opened the front door and looked over at the woman sitting in his couch. It hurt him to see her like this, but he was happy that she was back. Sheldon once again looked at the time and once he saw how late it was he quickly closed the door and locked it, leaving Amy alone in the cold apartment.

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 **Reed Clayton is based on a character in a game. I've changed his name and story a little but he is an** **Engineer in a futuristic game and he creates robots and AI's.**

 **Everything will be better explained in the next chapter. I try to update every Saturday or Sunday.**


	4. Chapter 4

**A/N: Disclaimer- The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady.**

 **I'm sorry for not updating last week. With Halloween and the birthday of my best friend I completely forgot about it and I didn't have enough time to write.**

 **Also I know both Sheldon and Amy are probably ooc and I apologize for that.**

* * *

 **Chapter 4  
** Amy stared at the closed door, reflecting on everything that had happened in the past few days. She still had many questions and wasn't sure if she wanted an answer for them. She had no idea what she should be feeling or what she was feeling at the moment. Ever since she had woken up she had been confused with her feelings. To her it felt like her brain didn't recognize them anymore or didn't know how the register them.

A deep sigh escaped her mouth as she pushed herself up from the couch. She figured that she should probably take a shower and put on some new clothes, since she hadn't changed since the day she had woken up.

Walking around the apartment she saw several pictures of the brown-haired woman again. The same woman who had all those horrifying looking injuries. She now realized this woman was probably her.

As she made her way down the hall she opened the first door she saw and entered a tidy looking children's room. Another picture of the woman was standing on the nightstand next to the pink, girlish bed. She took the picture from the nightstand and sat down on the bed. Her fingers ran down the simple frame as she stared at the picture. She seemed happy and familiar.

After having put the picture back on the nightstand and she had left the room she made her way over to the room across. This room was messier then the other had been. Once again papers were spread out on the ground. A big whiteboard was standing in the middle of the room. She didn't understand anything that was written on it.

She took a few papers from the ground and quickly scanned over the page. The first page showed the name of the project and its meaning. S.O.P.H.I.A. Series One Project Hyper Intelligent Android. The other information on the pages was mostly about how the project originated and what had gone wrong.

She spent the next half hour looking for something about her, however she only found something about another failed project, but there was very little information about that project.

After having searched for a longer amount of time she finally went to the last room in the hall. It was the bathroom. She did as Sheldon had recommended her and quickly took off her clothes and stepped under the warm water. As she was naked she looked down her body. It was hard to believe that this body wasn't real, it looked real to her.

When she heard the front door open, she quickly turned off the water and exited the shower. She grabbed a large towel and wrapped it around her body. Only now she realized that she hadn't grabbed new clothes.

"Amy?" She heard Sheldon say through the closed door. "Just a second." She replied as she grabbed her worn clothes and put them back on. After she had dressed and told Sheldon the door was open he opened it and closed the door behind him. She immediately took a step back, the close proximity made her uncomfortable.

"I brought someone with me, just be nice to her." Sheldon said. Amy frowned but nodded. Why wouldn't she be nice? She asked herself. Sheldon once again opened the door and walked out of the bathroom with Amy following him. "Nicola?" Sheldon asked.

"Yes?" A voice came from the children's bedroom. Sheldon made his way over to the room and opened the door. A young girl with dark brown hair and glasses on her face was sitting in the middle of the room, playing with a doll. The girl looked up expectantly to Sheldon. "I'd like you to meet someone." He stated. Sheldon took a step aside, leaving Amy awkwardly standing in the doorway of the girl her room and remained quiet.

The girl rose to her feet and walked over to Amy. She wrapped her arms around her and pressed her head against her legs. "You brought Mommy home." She said happily.

Amy looked up at Sheldon, not knowing what to do. Sheldon luckily noticed and told the girl to let her go. "Now Nicola, Amy isn't alright yet, she's still a little sick." Sheldon explained as he looked from Amy back to his daughter. "You mean she still hasn't recovered her memories and has no idea who we are, right?" The girl asked.

Amy was impressed by her manner of speaking, she figured that the child couldn't be much older than 4, yet she spoke like she had been speaking for years. She seemed like a very bright young child.

After Sheldon explained more about the situation he had left the room, leaving Amy and Nicola on their own. For the next hours the girl kept talking nonstop, about school, her toys, her friends and of course Sheldon. During dinner Sheldon had asked her about her day and she once again told the story about what had happened at school that day.

After dinner she continued talking, until her bed time. Amy remained in the living room as Sheldon brought her to bed. After a few minutes had passed he returned to the living room, to find Amy sitting on the couch once again, her arms wrapped around her legs and her head resting on her knees.

"I apologize, I know it's a lot to take in." Sheldon said as he made his way over to the kitchen and started making tea. "It's okay, she's a nice kid." Amy replied. Sheldon nodded for a moment. "She sure is, she got that from you." He stated. Amy didn't reply to that.

Sheldon made his way over to the couch, holding two cups of tea. He put them down on the table. "I'm guessing you'd like some answers now?" He asked as he sat down on the other side of the couch. "I would like some, yes." She quickly replied. "Very well." Sheldon said before letting out a soft sigh.

"About 8 years ago we had a son named Steven. He was a very bubbly and happy child, however that changed when he was only two years old. He was infected by something called the IMV virus. It's a virus that mainly attacks your brain and it slowly affects your brain. Scientists have no idea how it came into existence, how you get infected or how to cure it. Simply put we were just very unlucky people. Shortly after you became depressed, you hadn't worked in two years because you were always home with Steven so even after his death, you remained at home. You refused to eat or leave the apartment until a couple of months later Doctor Clayton visited you. He invited you for a project. He is an engineer who specialized in creating robots and AI's after his wife and daughter died. He was able to create the perfect body however he needed help with the brain. He couldn't figure out how to create the perfect environment for the brain and that's where you came in. You accepted his proposal and helped him with his project. I don't know a lot about the project, all I know is that you succeeded at the beginning but something went wrong and his brain became corrupt. You described him as a psychopath. By this time you were pregnant with our second child. Your project escaped and started targeting you. He was the one that killed you. It was a miracle that your brain was still intact and that Nicola survived the accident. I was the one who brought you back to Doctor Clayton and we decided to make you the new project. It's why your file said A.M.I.E. It stands for Advanced Mainframe Identity Engine. I worked with Doctor Clayton to get you back, but without your help it was harder than we thought. We've made several attempts already but we never got it right, until 3 days ago and now you're here." With that Sheldon ended his story. "Would you like some more tea?" He asked as he stood up from the couch and made his way over to the kitchen once again, leaving a stunned Amy sitting on the couch.

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 **Thank you for all the reviews so far!**


	5. Chapter 5

**A/N: Disclaimer- The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady.**

 **I won't be able to update this weekend, I'm going to England this weekend and sadly won't have any time to write.**

 **I'm sorry if there are some mistakes. I didn't have a lot of time to write this, but wanted to update before leaving for England.**

* * *

 **Chapter 5  
** Amy had no idea how to respond to all the new information she had gotten. It felt like her mind was in overdrive, trying to process all her new knowledge. She didn't want to believe him, but her rational mind kept her from it.

She remained quiet for a long time. Sheldon had returned with tea in the meantime and had sat down again. She was still staring at the table in front of her, trying to make sense of everything.

She wondered if she would ever get her memories and feelings back. She had had dreams, they had most likely been about the past, so she figured that maybe in time she would get her memories back. If you got her memories back, maybe she would also get her feelings back. She knew she could feel, she knew she felt emotions. Currently, she just didn't understand them. Everything felt new to her.

"Shouldn't I be tested? To make sure you didn't fail again?" She suddenly asked as she looked back up to Sheldon. She had quickly composed herself again and figured that she should ask some important questions now he was willing to talk. Her feelings and emotions could be pushed back right now.

Sheldon looked stunned by her question but also composed himself quickly. "Yes, you were supposed to stay at the lab, but as much as I admire Dr. Clayton for his work, I do not trust him." Sheldon stated after clearing his throat.

Amy nodded before looking away again. Why wouldn't Sheldon trust the man he had been working with for years? She must admit that when she spoke to him he didn't seem very friendly, but she didn't felt threatened by him. She had felt more threatened by Sheldon the day before, but that also might have been because of the lack of clothing.

The lack of sadness disturbed her a little. She felt like she should at least be sad about losing her memories but she wasn't. At least she couldn't describe it as sadness. "What went wrong with the previous project?" She asked.

Sheldon let out a sigh. "He couldn't feel empathy and most of his thoughts were cruel and disturbing. After you explained your desire to stop the project and shut the project down, he started seeing you as a potential threat, which ultimately let to your death." Sheldon explained.

Once again she didn't know how to respond to that. If the previous project had been a failure because of lack of emotions she just might end up as another failure. However she didn't think her thoughts were disturbing. She might have jumped quickly to the conclusion that Sheldon would harm her the day before, but who could blame her for that, right?

She let out an unnerving breath before abruptly standing up. "I would like to sleep now, I do not wish to continue this conversation." She stated with a monotone voice. Sheldon quickly stood up as well. "Uhm.. okay.. sure.. Are you okay?" He asked worriedly. She nodded before looking around her. "Where do I sleep?" She asked, ignoring his question.

Sheldon took the empty cups from the table and brought them to the kitchen. "You can sleep in my bed, I will sleep on the couch. I know you've been in my room, so you know where to find it." He said as he cleaned the cups before putting them in the dishwasher.

* * *

After Sheldon had explained his night rituals and they had successfully done them, Amy was sitting in bed and Sheldon continued to stare at her. "Are you okay? I understand that this was-" "I'm fine." Amy interrupted him. She pulled up the blankets over the lower half of her body. "You can go now, as I said earlier, I wish to sleep now." She once again said.

Sheldon reluctantly left the room and closed the door. Amy let out a relieved sigh when he was gone. She felt uneasy about treating Sheldon that way but she was scared that they would see her as a failure as well and try to shut her down. She knew there were many things she didn't know yet. There were many things that should scare her, but right now the only thing she feared would be shut down or killed or whatever it was that would happen to her. She wanted to learn, gain knowledge, experience new things. She wanted to learn more about the little girl in the room next to her, she had been interesting and seemed very nice and excited.

She rested her head on the pillow, which Sheldon had left her and pulled up the blankets. She closed her eyes and luckily she fell asleep quickly.

* * *

A chill ran down Amy her spine as she opened the door. At first she had no idea where she was, but after looking around she realized she was in a class room and she was late. Most lights were turned off except for a small lamp at the back of the room. All the other students was gathered around the table, surrounded by light.

She took a deep breath of air before making her way over to join the others. Somehow she knew that she wouldn't like what she saw at the table. The others made room for her to stand in the circle. The moment she rested her eyes on the table she saw a brown haired girl laying naked on the table and she knew it was her. She was heavily beaten and unreadable words were written on her body. The other people had smug looks on their faces, they seemed to enjoy this situation.

The girl on the table suddenly opened her eyes and looked straight at her. She quickly took a step backwards. Everyone else in the room had disappeared. "What are you looking at?" The girl growled as she suddenly sat up. Amy once again took a few steps back. The girl suddenly threw herself at Amy. She got knocked back and fell, her head hit the ground and everything became black.

When she opened her eyes again she was in a grass field. It suddenly was a beautiful day, the sun was shining bright. She could feel the warmth of the sun on her skin and a soft breeze of cool wind. She was surrounded by flowers and a lake. Everything was perfect.

She was holding Nicola's hand, watching the fish jump out of the large pond. Nicola looked up at her and repeatedly said: "It's ok." She looked down at the girl, into her gorgeous bright blue eyes and saw. A deafening sound came from right behind her, shocking her for a moment. She felt Nicola's hand slip out of hers and watched her fall to the ground before hearing the second shot. The shooter had turned and had also shot her.

She felt an incredible pain in the back of her head, something like she had never felt before. She fell backward but instead of hitting the grass, she landed on a rock like table. She sat up and saw a room filled with hanging bodies. One of which being Nicola, the other were people she had met in the previous days. They were all screaming. Fear overcame her and she curled up in a little ball and cried, knowing that she couldn't do anything.

When they temporarily stopped she looked up again. She saw Sheldon dragging himself towards her, holding a bat with nails sticking out of it. The screaming started again, but this time not only from the people she knew but also from her. She remained screaming before finally waking up.

She sat up straight, her eyes were wide open and she was breathing heavily. Her heart was pounding in her chest and she couldn't stop shaking. She was almost hyperventilating. Her throat was sore and she was drenched in sweat. It took a moment before she started to notice her surroundings.

She heard Sheldon banging on the door, asking to be let in. The door suddenly opened and he hurried his way inside, closely followed by Nicola who had also woken up.

Seconds later a faceless man entered the room. With a confused look on her face she looked at all of the people in the room. She tried to ask why they were all here, but no words came from her mouth.

The faceless man grabbed Sheldon by his throat and pushed him with ease against the wall. "You didn't think I'd ever let you escape, right?" The faceless man remarked with a smug grin on his face. He pushed his hand into Sheldon's back and effortlessly ripped out his spine. She was bound to bed, unable to do anything.

Once he had dropped Sheldon's lifeless body he came towards her. Suddenly able to move, she grabbed Nicola's hand and pulled her with her off the bed. She made her way over to door which led to the hallway. She opened the door and immediately stepped into it, pulling Nicola with her. She closed the bedroom door behind her and looked around for an escape. There was none.

She was now standing in a closet and Nicola had turned to dust and disappeared. She could hear the faint sounds of a TV playing in the distance. The only light was coming through the cracks in the door, caused by the lights of the TV. She tried to open the door but it was locked.

Suddenly she managed to open the door. However as she did she got a dreadful feeling. She was viewing the earth from space while everything twisted and crushed together into a tiny ball, before disappearing altogether. The world had ended and she was viewing it from space in an uncomfortable closet.

She remained standing there for several moments, contemplating what she was going to do. Standing here wouldn't do her any good so she did the only other thing she could think of. She took a deep breath before stepping out of the closet, falling into the unknown darkness.

* * *

 **The dream Amy has is based on a dream I had a couple of years ago.**

 **Once again thank you for all the reviews and favorites so far!**


	6. Chapter 6

**A/N: Disclaimer- The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady.**

 **I'm so sorry for the long wait! I had to design and write a report about my internship which had to be at least 40 pages. Pokemon Sun &Moon came out. My mother came home for the holidays. I went to England. So all in all my past few weeks have been very busy and I sadly didn't have a lot of time to write.**

 **I'll try to write as often as possible, but with my upcoming exams I probably won't be able to write or update a lot.  
**

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Chapter 6

Abruptly, Amy sat up in the bed. She quickly turned on the lamp on the nightstand and an unnerving breath escaped her mouth. She pulled up the sheets in an attempt to calm down, but the soft blanket did little to comfort her. She didn't understand why she kept having these strange dreams. She figured that they must contain some part of truth or maybe it was just her brain trying to make sense of the lost memories.

Once she had her breathing under control again she glanced over at the clock on the nightstand. She could read 3:30AM in bright red numbers. She slowly laid her head back down on the pillow behind her and curled up to her right side to watch the numbers change to 3:31AM.

As she was laying in the darkness she started wondering about what Sheldon has said. Why had she been brought back? Why had they been working on artificial bodies when Steven's brain had been damaged and not his body? And what happened to the escaped project?

Questions were swirling around in her head when suddenly a feeling of dread overcame her. What if he was still out there and was still trying to harm her? She might not know who she is or remember anything, but she knew one thing for sure. She wanted to live and she would do whatever it took to get that.

With that in mind she pushed herself up into a sitting position and glanced over at the clock once again. 4:02AM. She put her feet on the cold grounded and stood up, letting the blanket fall down to her feet. She needed more answers, sleep be damned.

Quietly, she walked down the door. She did not want to wake the little girl, sleeping down the hall. As she came into the living room she saw Sheldon curled up on the couch. Without a doubt she walked over to him and stopped right in front of the couch. "Sheldon." She said with a hushed voice.

When he didn't reply she said his name again, this time a little louder. He stirred but once again did not wake up. She lightly tapped his arm and again said his name. This time he suddenly sat up and said danger 3 times very loudly.

She jerked her hand back and looked down at him with a shocked expression on her face. "What's wrong?" he asked with a drowsy voice. "I need you to answer some of my questions." She stated as she sat down in the comfy chair, next to the couch.

Sheldon let out a sigh as he looked down at his watch. "It's the middle of the night, can't this wait?" He asked as he watched her make herself comfortable. She shook her head. "No, sleep is eluding me and even when I do sleep I keep having strange dreams."

"Very well." He said as he pushed himself up into a sitting position. "What do you want to know?" He asked. Amy looked down at her hands before nervously looking up at his face. "Euhm.. Well.. why did you bring me back? I mean I'm grateful, I guess? But it does make me wonder what you want from me and why I'm here." She explained.

"I already expected this question." He said with a smile on his face. "I wanted you back because I love you and wanted Nicola to know her mother. I'm afraid Doctor Clayton's reasons are less noble. He wants to continue using you because of your knowledge of the brain. He is convinced that your memories will come back to you and you once again will be the brilliant scientist you once were." Sheldon explained.

Amy nodded for a short moment before asking her next question. "Why were we working on artificial bodies when Steven's brain was damaged?" She asked with a slight frown on her face.

"Because not only did you manage to create the perfect environment for a human brain, you also perfected Doctor Clayton's artificial brains and managed to combine the two of them, depending on how severe the damage is of course." She stated matter-of-factly.

"What happened to the escaped project?" She asked, now a little insecure. As Sheldon's expression changed she knew that she would not like the answer.

"We have no idea, we do not know where he currently is. I do not want to frighten you but Doctor Clayton did mention that he might be coming for you. I think Doctor Clayton knows more about his whereabouts.

For the next few hours Amy continued asked questions and Sheldon answered them eagerly. She mostly asked about the past, about how her life had been and what she had been like. However they were interrupted by Nicola entering the living room. She greeted both Sheldon and Amy with a kiss on their cheeks. Amy was a little taken aback from this but quickly pulled herself together as she realized that this was probably a normal thing to do for a child.

Sheldon got off from the couch and told them he was going to make breakfast. Before Nicola could ask what they had been talking about Sheldon told her to wash up, since they were already running late. Within half an hour both Sheldon and Nicola had dressed up and eaten breakfast. Amy was still eating when Sheldon announced that he had to take her to school and would be back soon.

Before she knew it, she was once again alone in the apartment.

The next couple of weeks flew by in a haze. Amy got to know Sheldon and Nicola better and often played games with them. Nicola absolutely adored Amy, even though it was obvious that she wasn't used to the cheerfulness of the child. Sheldon also slowly seemed to become happier as the weeks progressed. Amy learned more about how she was created and her dreams started to make more sense. Her memories however, remained for the most part forgotten. They had not seen Doctor Clayton since the day they had left the lab, but Sheldon had spoken to him a couple of times on the phone.

One day while Nicola was at school and Sheldon had gone to the lab to discuss something with Doctor Clayton, Amy was quietly sitting on the couch reading a book, until there was a knock on the door. She reluctantly closed her book and got off the couch. She quickly walked over to the door and without a second opened it.

Two people were standing in the hall. A gorgeous woman with beautiful wavy blond hair stepped forward and pulled her into a hug while a blond-haired man with clear green eyes remained in standing in the hall. "Oh Amy I'm so happy to see you! When Sheldon told me what he had done I didn't believe him, yet here you are!" she exclaimed. Amy felt her shoulder getting wet from the woman's tears. She pushed herself out of the woman's grip and quickly took a step backwards.

"Who are you?" Amy asked as she grabbed the side of the door so she could close it in case something happened. The man rested his arm on the woman's forearm and stopped her from 'attacking' Amy once again.

"Miss Hofstadter, I don't think she recognized you, maybe you should tell her who you are before forcing her into physical contact again." The man spoke. Amy was grateful that the man had noticed her obvious discomfort and lack of knowledge about the woman.

"Yes of course." The woman said as she pulled herself together. "My name is Penny Hofstadter, I used to be your best friend." She said as she pushed some hair out of her face. "And this is my assistant Hal Hobbes." She gestured at the man next to her. "It's a pleasure to meet you ma'am, I've heard many good things about you."

Amy wasn't sure what to do. She did not know these people and Sheldon had told her many times that she had to be careful. She mentally scolded herself for opening the door in the first place. Penny interrupted her thoughts when she suddenly spoke again. "You really have no memory at all?" She asked to which Amy shook her head.

"How about we come back when Doctor Cooper is also present?" He suggested to penny. Penny reluctantly agreed. They said their goodbyes but before they had made it down the flight of stairs Amy called them back up.

"You can come in, I'm sure Sheldon doesn't mind. If you want to you can tell me more about yourself." Amy offered.

When they had both settled down on the couch, tea was made and Amy was sitting on the beige chair again an awkward silence arose. Amy started to regret inviting them in. She had been praised several times for her intelligence but so far she doubted if she truly was that intelligent.

Eventually Hal broke the silence. "Why don't you tell her about how you met?" Hal said softly. Penny nodded quickly as she started explaining how they had met and how they had become friends.

After some time Sheldon finally came home, causing Penny to jump up from the couch and forcing him into a hug. "Penny, please untangle yourself from me." Sheldon said grumpily. "I'm just happy to see you Sheldon!" Penny exclaimed happily as she finally let him go.

"Yes, it's also good to see you." He said while taking off his coat. "I see you've met Amy." Sheldon stated.

In the meantime Amy had gotten up from the chair and also made a cup of tea for Sheldon. She put it down on the small table before taking her place once again on the couch. "She's wonderful Sheldon! I did not believe you when you told us what you were going to do, but I'm happy you succeeded!" She beamed. "She looks exactly like the real Amy!" Penny continued.

A frown appeared on her face as she heard Penny's words. She agreed that it was wonderful work what they had done, but that did not mean it had to be stated like that. She felt like a real person and did not appreciate the blond her words.

Before she could voice her complaints Sheldon spoke. "She is the real Amy, her body might be artificial but it's truly her in there."

For the first time since she had awoken she felt a sense of safety. Of one thing she was certain if Sheldon truly believed that she was the real Amy, the Amy he loved, he would never try to harm her and would always protect her.

A smile appeared on her face as she looked over at Sheldon. "Thank you Sheldon." She mouthed before looking back at Penny.

Penny continued talking about her life for the next hour. She told them how her marriage with Leonard was, how their son was doing in school and about how after being a pharmaceutical sales rep did not go well she decided to try acting again and this time was successful.

When Sheldon finally announced that it was time for them to go Penny made an appointment with Amy to go have lunch somewhere in the following week. Amy didn't feel like going, she wanted to stay in the safe environment of the apartment but Sheldon encouraged her to go. After some good arguments from Sheldon, Amy reluctantly agreed and they both said their goodbyes to Penny and Hal.

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 **Once again thank you for all the reviews and favorites! I'll try to update next week.**


	7. Chapter 7

**A/N: Disclaimer- The Big Bang Theory belongs to CBS, Warner Bros, Chuck Lorre and Bill Prady.**

 **Hello hello! I know this is a short chapter but I felt bad for letting you wait for such a long time. I was planning on writing more but I simply don't have time right now. I'm in the middle of my exams and the next time I'll have time to write will probably be in 3 weeks, after my birthday and first exam.**

 **This chapter hasn't been read by my beta reader, she also didn't have time because of her exams. I'm sorry if there are some mistakes!**

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Everyone wanted something from her. The little girl, as kind as she was, wanted to spend all her free time with Amy and it started to work on her nerves. Sheldon did regular checkups on her body and tests on her mind. She felt like she had no privacy.

She hadn't told Sheldon about her fears or her dreams yet. Her thoughts were the only thing that were private. The only time she felt like she wasn't on edge were the times that Sheldon was working, Nicola was at school and she had the apartment to herself.

However, in the following weeks that changed. Sheldon remained in contact with Penny. The actress wanted to spend more time with her and take her outside for some coffee sometime. Sheldon seemed very keen on the idea that they would get reacquainted, Amy on the other hand wasn't. She didn't want to leave the safety of the apartment. She had grown accustomed to everything there.

She feared what would happen once she would step outside the front door. Only once had she been outside since she had awoken. Sheldon seemed to understand her fears at first and agreed to postpone the appointment, but after another two weeks Sheldon seemed to think she was ready.

For the past weeks she had worn simple skirts, occasionally leggings with one of Sheldon's old t-shirts above it. His red Flash t-shirt was her favorite, it was old but soft and it seemed familiar.

Sheldon had brought some new clothes home for her appointment with Penny. However, on the day itself, she refused to wear them. She wanted to wear the clothes she felt comfortable in. She didn't understand why she suddenly had to change her attire. After some negotiation Sheldon finally agreed to let her wear his flash shirt, with a cardigan above it.

Soon after Sheldon left to bring Nicola to school and to go to work there was a knock on the door. Amy let out a nervous sigh before opening the front door. She knew she should have expected it but the moment the blonde woman pulled her into her arms she once again stiffened.

"Hello Penny," Amy said. She turned her attention to Hal, the assistant. "Hello Hal." Hal gave her a curt nod. After the woman finally released her she laughed. "I'm sorry," she said as she composed herself. "It's still such an amazing thing that you're back!"

Amy nodded for a short moment and grabbed the bag Sheldon had prepared for her, he said it contained everything she needed. "Are you ready to go?" Penny exclaimed happily.

Once again a nervous breath escaped her mouth. She looked behind her in the apartment, wishing that she could simply close to door in front of the two people, but knew that that wasn't acceptable. Amy turned her attention back to Penny and Hal and forced a smile on her face. She took a quick step forward and closed the door behind her.

She released the breath that she had apparently been holding. The world hadn't imploded yet, but who knew what would happen once she would leave the building and actually go outside.


End file.
